期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 103, 期 33, 页码 12457-12462出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0601180103
关键词
functional genomics; genome tiling microarrays; model-based probe analysis; transcription regulation
资金
- NHGRI NIH HHS [R01 HG004069-01, R01 HG004069] Funding Source: Medline
- NIDDK NIH HHS [T90 DK070078-01, T90 DK070078] Funding Source: Medline
We propose a fast and powerful analysis algorithm, titled Modelbased Analysis of Tiling-arrays (MAT), to reliably detect regions enriched by transcription factor chromatin immunoprecipitation (ChIP) on Affymetrix tiling arrays (ChIP-chip). MAT models the baseline probe behavior by considering probe sequence and copy number on each array. It standardizes the probe value through the probe model, eliminating the need for sample normalization. MAT uses an innovative function to score regions for ChIP enrichment, which allows robust P value and false discovery rate calculations. MAT can detect ChIP regions from a single ChIP sample, multiple ChIP samples, or multiple ChIP samples with controls with increasing accuracy. The single-array ChIP region detection feature minimizes the time and monetary costs for laboratories newly adopting ChIP-chip to test their protocols and antibodies and allows established ChIP-chip laboratories to identify samples with questionable quality that might contaminate their data. MAT is developed in open-source Python and is available at http://chip. dfci.harvard.edu/-wli/MAT. The general framework presented here can be extended to other oligonucleoticle microarrays and tiling array platforms.
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